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libcifpp
Commit 19210df6 by Maarten L. Hekkelman
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Fix parsing mmCIF files with an unquoted string ??

parent 15c57307
Showing with 651 additions and 657 deletions
CMakeLists.txt
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
cmake_minimum_required(VERSION 3.16) cmake_minimum_required(VERSION 3.16)
# set the project name # set the project name
project(cifpp VERSION 3.0.2 LANGUAGES CXX) project(cifpp VERSION 3.0.4 LANGUAGES CXX)
list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake") list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
......
changelog
Version 3.0.4
- Fix in mmCIF parser, now correctly handles the unquoted
string ??
Version 3.0.3 Version 3.0.3
- Better configuration checks, for atomic e.g. - Better configuration checks, for atomic e.g.
- Fixed a problem introduced in refactoring mmcif::Atom - Fixed a problem introduced in refactoring mmcif::Atom
...@@ -17,6 +21,9 @@ Version 3.0.0 ...@@ -17,6 +21,9 @@ Version 3.0.0
- Upgraded mmcif::Structure - Upgraded mmcif::Structure
- various other small fixes - various other small fixes
Version 2.0.5
- Backporting updated CMakeLists.txt file
Version 2.0.4 Version 2.0.4
- Reverted a too strict test when reading cif files. - Reverted a too strict test when reading cif files.
......
include/cif++/CifParser.hpp
/*- /*-
* SPDX-License-Identifier: BSD-2-Clause * SPDX-License-Identifier: BSD-2-Clause
* *
* Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
* *
* Redistribution and use in source and binary forms, with or without * Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met: * modification, are permitted provided that the following conditions are met:
* *
* 1. Redistributions of source code must retain the above copyright notice, this * 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer * list of conditions and the following disclaimer
* 2. Redistributions in binary form must reproduce the above copyright notice, * 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation * this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution. * and/or other materials provided with the distribution.
* *
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
...@@ -139,7 +139,7 @@ class SacParser ...@@ -139,7 +139,7 @@ class SacParser
int getNextChar(); int getNextChar();
void retract(); void retract();
void restart(); int restart(int start);
CIFToken getNextToken(); CIFToken getNextToken();
void match(CIFToken token); void match(CIFToken token);
...@@ -181,8 +181,9 @@ class SacParser ...@@ -181,8 +181,9 @@ class SacParser
eStateTextField, eStateTextField,
eStateFloat = 100, eStateFloat = 100,
eStateInt = 110, eStateInt = 110,
// eStateNumericSuffix = 200, eStateValue = 300,
eStateValue = 300 eStateDATA,
eStateSAVE
}; };
std::istream &mData; std::istream &mData;
...@@ -191,7 +192,6 @@ class SacParser ...@@ -191,7 +192,6 @@ class SacParser
bool mValidate; bool mValidate;
uint32_t mLineNr; uint32_t mLineNr;
bool mBol; bool mBol;
int mState, mStart;
CIFToken mLookahead; CIFToken mLookahead;
std::string mTokenValue; std::string mTokenValue;
CIFValueType mTokenType; CIFValueType mTokenType;
......
src/CifParser.cpp
/*- /*-
* SPDX-License-Identifier: BSD-2-Clause * SPDX-License-Identifier: BSD-2-Clause
* *
* Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
* *
* Redistribution and use in source and binary forms, with or without * Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met: * modification, are permitted provided that the following conditions are met:
* *
* 1. Redistributions of source code must retain the above copyright notice, this * 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer * list of conditions and the following disclaimer
* 2. Redistributions in binary form must reproduce the above copyright notice, * 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation * this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution. * and/or other materials provided with the distribution.
* *
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
...@@ -42,7 +42,7 @@ namespace cif ...@@ -42,7 +42,7 @@ namespace cif
const uint32_t kMaxLineLength = 132; const uint32_t kMaxLineLength = 132;
const uint8_t kCharTraitsTable[128] = { const uint8_t kCharTraitsTable[128] = {
// 0 1 2 3 4 5 6 7 8 9 a b c d e f // 0 1 2 3 4 5 6 7 8 9 a b c d e f
14, 15, 14, 14, 14, 15, 15, 14, 15, 15, 15, 15, 15, 15, 15, 15, // 2 14, 15, 14, 14, 14, 15, 15, 14, 15, 15, 15, 15, 15, 15, 15, 15, // 2
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 15, 15, 15, 15, // 3 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 15, 15, 15, 15, // 3
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, // 4 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, // 4
...@@ -151,23 +151,26 @@ void SacParser::retract() ...@@ -151,23 +151,26 @@ void SacParser::retract()
mTokenValue.pop_back(); mTokenValue.pop_back();
} }
void SacParser::restart()
int SacParser::restart(int start)
{ {
int result = 0;
while (not mTokenValue.empty()) while (not mTokenValue.empty())
retract(); retract();
switch (mStart) switch (start)
{ {
case eStateStart: case eStateStart:
mState = mStart = eStateFloat; result = eStateFloat;
break; break;
case eStateFloat: case eStateFloat:
mState = mStart = eStateInt; result = eStateInt;
break; break;
case eStateInt: case eStateInt:
mState = mStart = eStateValue; result = eStateValue;
break; break;
default: default:
...@@ -175,6 +178,8 @@ void SacParser::restart() ...@@ -175,6 +178,8 @@ void SacParser::restart()
} }
mBol = false; mBol = false;
return result;
} }
void SacParser::match(SacParser::CIFToken t) void SacParser::match(SacParser::CIFToken t)
...@@ -191,7 +196,7 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -191,7 +196,7 @@ SacParser::CIFToken SacParser::getNextToken()
CIFToken result = eCIFTokenUnknown; CIFToken result = eCIFTokenUnknown;
int quoteChar = 0; int quoteChar = 0;
mState = mStart = eStateStart; int state = eStateStart, start = eStateStart;
mBol = false; mBol = false;
mTokenValue.clear(); mTokenValue.clear();
...@@ -201,7 +206,7 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -201,7 +206,7 @@ SacParser::CIFToken SacParser::getNextToken()
{ {
auto ch = getNextChar(); auto ch = getNextChar();
switch (mState) switch (state)
{ {
case eStateStart: case eStateStart:
if (ch == kEOF) if (ch == kEOF)
...@@ -209,27 +214,23 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -209,27 +214,23 @@ SacParser::CIFToken SacParser::getNextToken()
else if (ch == '\n') else if (ch == '\n')
{ {
mBol = true; mBol = true;
mState = eStateWhite; state = eStateWhite;
} }
else if (ch == ' ' or ch == '\t') else if (ch == ' ' or ch == '\t')
mState = eStateWhite; state = eStateWhite;
else if (ch == '#') else if (ch == '#')
mState = eStateComment; state = eStateComment;
else if (ch == '.')
mState = eStateDot;
else if (ch == '_') else if (ch == '_')
mState = eStateTag; state = eStateTag;
else if (ch == ';' and mBol) else if (ch == ';' and mBol)
mState = eStateTextField; state = eStateTextField;
else if (ch == '\'' or ch == '"') else if (ch == '\'' or ch == '"')
{ {
quoteChar = ch; quoteChar = ch;
mState = eStateQuotedString; state = eStateQuotedString;
} }
else if (ch == '?')
mState = eStateQuestionMark;
else else
restart(); state = start = restart(start);
break; break;
case eStateWhite: case eStateWhite:
...@@ -237,7 +238,7 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -237,7 +238,7 @@ SacParser::CIFToken SacParser::getNextToken()
result = eCIFTokenEOF; result = eCIFTokenEOF;
else if (not isspace(ch)) else if (not isspace(ch))
{ {
mState = eStateStart; state = eStateStart;
retract(); retract();
mTokenValue.clear(); mTokenValue.clear();
} }
...@@ -248,7 +249,7 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -248,7 +249,7 @@ SacParser::CIFToken SacParser::getNextToken()
case eStateComment: case eStateComment:
if (ch == '\n') if (ch == '\n')
{ {
mState = eStateStart; state = eStateStart;
mBol = true; mBol = true;
mTokenValue.clear(); mTokenValue.clear();
} }
...@@ -258,44 +259,19 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -258,44 +259,19 @@ SacParser::CIFToken SacParser::getNextToken()
error("invalid character in comment"); error("invalid character in comment");
break; break;
case eStateQuestionMark:
if (isNonBlank(ch))
mState = eStateValue;
else
{
retract();
result = eCIFTokenValue;
mTokenValue.clear();
mTokenType = eCIFValueUnknown;
}
break;
case eStateDot:
if (isdigit(ch))
mState = eStateFloat + 2;
else if (isspace(ch))
{
retract();
result = eCIFTokenValue;
mTokenType = eCIFValueInapplicable;
}
else
mState = eStateValue;
break;
case eStateTextField: case eStateTextField:
if (ch == '\n') if (ch == '\n')
mState = eStateTextField + 1; state = eStateTextField + 1;
else if (ch == kEOF) else if (ch == kEOF)
error("unterminated textfield"); error("unterminated textfield");
else if (not isAnyPrint(ch) and cif::VERBOSE >= 0) else if (not isAnyPrint(ch))
// error("invalid character in text field '" + string({ static_cast<char>(ch) }) + "' (" + to_string((int)ch) + ")"); // error("invalid character in text field '" + string({ static_cast<char>(ch) }) + "' (" + to_string((int)ch) + ")");
std::cerr << "invalid character in text field '" << std::string({static_cast<char>(ch)}) << "' (" << ch << ") line: " << mLineNr << std::endl; std::cerr << "invalid character in text field '" << std::string({static_cast<char>(ch)}) << "' (" << ch << ") line: " << mLineNr << std::endl;
break; break;
case eStateTextField + 1: case eStateTextField + 1:
if (isTextLead(ch) or ch == ' ' or ch == '\t') if (isTextLead(ch) or ch == ' ' or ch == '\t')
mState = eStateTextField; state = eStateTextField;
else if (ch == ';') else if (ch == ';')
{ {
assert(mTokenValue.length() >= 2); assert(mTokenValue.length() >= 2);
...@@ -313,7 +289,7 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -313,7 +289,7 @@ SacParser::CIFToken SacParser::getNextToken()
if (ch == kEOF) if (ch == kEOF)
error("unterminated quoted string"); error("unterminated quoted string");
else if (ch == quoteChar) else if (ch == quoteChar)
mState = eStateQuotedStringQuote; state = eStateQuotedStringQuote;
else if (not isAnyPrint(ch)) else if (not isAnyPrint(ch))
error("invalid character in quoted string"); error("invalid character in quoted string");
break; break;
...@@ -331,7 +307,7 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -331,7 +307,7 @@ SacParser::CIFToken SacParser::getNextToken()
else if (ch == quoteChar) else if (ch == quoteChar)
; ;
else if (isAnyPrint(ch)) else if (isAnyPrint(ch))
mState = eStateQuotedString; state = eStateQuotedString;
else if (ch == kEOF) else if (ch == kEOF)
error("unterminated quoted string"); error("unterminated quoted string");
else else
...@@ -349,12 +325,12 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -349,12 +325,12 @@ SacParser::CIFToken SacParser::getNextToken()
case eStateFloat: case eStateFloat:
if (ch == '+' or ch == '-') if (ch == '+' or ch == '-')
{ {
mState = eStateFloat + 1; state = eStateFloat + 1;
} }
else if (isdigit(ch)) else if (isdigit(ch))
mState = eStateFloat + 1; state = eStateFloat + 1;
else else
restart(); state = start = restart(start);
break; break;
case eStateFloat + 1: case eStateFloat + 1:
...@@ -362,9 +338,9 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -362,9 +338,9 @@ SacParser::CIFToken SacParser::getNextToken()
// mState = eStateNumericSuffix; // mState = eStateNumericSuffix;
// else // else
if (ch == '.') if (ch == '.')
mState = eStateFloat + 2; state = eStateFloat + 2;
else if (tolower(ch) == 'e') else if (tolower(ch) == 'e')
mState = eStateFloat + 3; state = eStateFloat + 3;
else if (isWhite(ch) or ch == kEOF) else if (isWhite(ch) or ch == kEOF)
{ {
retract(); retract();
...@@ -372,16 +348,13 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -372,16 +348,13 @@ SacParser::CIFToken SacParser::getNextToken()
mTokenType = eCIFValueInt; mTokenType = eCIFValueInt;
} }
else else
restart(); state = start = restart(start);
break; break;
// parsed '.' // parsed '.'
case eStateFloat + 2: case eStateFloat + 2:
// if (ch == '(') // numeric???
// mState = eStateNumericSuffix;
// else
if (tolower(ch) == 'e') if (tolower(ch) == 'e')
mState = eStateFloat + 3; state = eStateFloat + 3;
else if (isWhite(ch) or ch == kEOF) else if (isWhite(ch) or ch == kEOF)
{ {
retract(); retract();
...@@ -389,30 +362,27 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -389,30 +362,27 @@ SacParser::CIFToken SacParser::getNextToken()
mTokenType = eCIFValueFloat; mTokenType = eCIFValueFloat;
} }
else else
restart(); state = start = restart(start);
break; break;
// parsed 'e' // parsed 'e'
case eStateFloat + 3: case eStateFloat + 3:
if (ch == '-' or ch == '+') if (ch == '-' or ch == '+')
mState = eStateFloat + 4; state = eStateFloat + 4;
else if (isdigit(ch)) else if (isdigit(ch))
mState = eStateFloat + 5; state = eStateFloat + 5;
else else
restart(); state = start = restart(start);
break; break;
case eStateFloat + 4: case eStateFloat + 4:
if (isdigit(ch)) if (isdigit(ch))
mState = eStateFloat + 5; state = eStateFloat + 5;
else else
restart(); state = start = restart(start);
break; break;
case eStateFloat + 5: case eStateFloat + 5:
// if (ch == '(')
// mState = eStateNumericSuffix;
// else
if (isWhite(ch) or ch == kEOF) if (isWhite(ch) or ch == kEOF)
{ {
retract(); retract();
...@@ -420,14 +390,14 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -420,14 +390,14 @@ SacParser::CIFToken SacParser::getNextToken()
mTokenType = eCIFValueFloat; mTokenType = eCIFValueFloat;
} }
else else
restart(); state = start = restart(start);
break; break;
case eStateInt: case eStateInt:
if (isdigit(ch) or ch == '+' or ch == '-') if (isdigit(ch) or ch == '+' or ch == '-')
mState = eStateInt + 1; state = eStateInt + 1;
else else
restart(); state = start = restart(start);
break; break;
case eStateInt + 1: case eStateInt + 1:
...@@ -438,35 +408,11 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -438,35 +408,11 @@ SacParser::CIFToken SacParser::getNextToken()
mTokenType = eCIFValueInt; mTokenType = eCIFValueInt;
} }
else else
restart(); state = start = restart(start);
break; break;
// case eStateNumericSuffix:
// if (isdigit(ch))
// mState = eStateNumericSuffix + 1;
// else
// restart();
// break;
//
// case eStateNumericSuffix + 1:
// if (ch == ')')
// {
// result = eCIFTokenValue;
// mTokenType = eCIFValueNumeric;
// }
// else if (not isdigit(ch))
// restart();
// break;
case eStateValue: case eStateValue:
if (isNonBlank(ch)) if (ch == '_')
mState = eStateValue + 1;
else
error("invalid character at this position");
break;
case eStateValue + 1:
if (ch == '_') // first _, check for keywords
{ {
std::string s = toLowerCopy(mTokenValue); std::string s = toLowerCopy(mTokenValue);
...@@ -476,23 +422,40 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -476,23 +422,40 @@ SacParser::CIFToken SacParser::getNextToken()
result = eCIFTokenSTOP; result = eCIFTokenSTOP;
else if (s == "loop_") else if (s == "loop_")
result = eCIFTokenLOOP; result = eCIFTokenLOOP;
else if (s == "data_" or s == "save_") else if (s == "data_")
mState = eStateValue + 2; {
state = eStateDATA;
continue;
}
else if (s == "save_")
{
state = eStateSAVE;
continue;
}
} }
else if (not isNonBlank(ch))
if (result == eCIFTokenUnknown and not isNonBlank(ch))
{ {
retract(); retract();
result = eCIFTokenValue; result = eCIFTokenValue;
mTokenType = eCIFValueString;
if (mTokenValue == ".")
mTokenType = eCIFValueInapplicable;
else if (mTokenValue == "?")
{
mTokenType = eCIFValueUnknown;
mTokenValue.clear();
}
} }
break; break;
case eStateValue + 2: case eStateDATA:
case eStateSAVE:
if (not isNonBlank(ch)) if (not isNonBlank(ch))
{ {
retract(); retract();
if (tolower(mTokenValue[0]) == 'd') if (state == eStateDATA)
result = eCIFTokenDATA; result = eCIFTokenDATA;
else else
result = eCIFTokenSAVE; result = eCIFTokenSAVE;
...@@ -521,6 +484,7 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -521,6 +484,7 @@ SacParser::CIFToken SacParser::getNextToken()
return result; return result;
} }
DatablockIndex SacParser::indexDatablocks() DatablockIndex SacParser::indexDatablocks()
{ {
DatablockIndex index; DatablockIndex index;
......
test/unit-test.cpp
/*- /*-
* SPDX-License-Identifier: BSD-2-Clause * SPDX-License-Identifier: BSD-2-Clause
* *
* Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
* *
* Redistribution and use in source and binary forms, with or without * Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met: * modification, are permitted provided that the following conditions are met:
* *
* 1. Redistributions of source code must retain the above copyright notice, this * 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer * list of conditions and the following disclaimer
* 2. Redistributions in binary form must reproduce the above copyright notice, * 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation * this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution. * and/or other materials provided with the distribution.
* *
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
...@@ -31,36 +31,35 @@ ...@@ -31,36 +31,35 @@
#include <stdexcept> #include <stdexcept>
// #include "cif++/DistanceMap.hpp" // #include "cif++/DistanceMap.hpp"
#include "cif++/Cif++.hpp"
#include "cif++/BondMap.hpp" #include "cif++/BondMap.hpp"
#include "cif++/Cif++.hpp"
#include "cif++/CifValidator.hpp" #include "cif++/CifValidator.hpp"
namespace tt = boost::test_tools; namespace tt = boost::test_tools;
std::filesystem::path gTestDir = std::filesystem::current_path(); // filled in first test
std::filesystem::path gTestDir = std::filesystem::current_path(); // filled in first test
// -------------------------------------------------------------------- // --------------------------------------------------------------------
cif::File operator""_cf(const char* text, size_t length) cif::File operator""_cf(const char *text, size_t length)
{ {
struct membuf : public std::streambuf struct membuf : public std::streambuf
{ {
membuf(char* text, size_t length) membuf(char *text, size_t length)
{ {
this->setg(text, text, text + length); this->setg(text, text, text + length);
} }
} buffer(const_cast<char*>(text), length); } buffer(const_cast<char *>(text), length);
std::istream is(&buffer); std::istream is(&buffer);
return cif::File(is); return cif::File(is);
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
bool init_unit_test() bool init_unit_test()
{ {
cif::VERBOSE = 1; cif::VERBOSE = 1;
// not a test, just initialize test dir // not a test, just initialize test dir
if (boost::unit_test::framework::master_test_suite().argc == 2) if (boost::unit_test::framework::master_test_suite().argc == 2)
...@@ -79,9 +78,9 @@ bool init_unit_test() ...@@ -79,9 +78,9 @@ bool init_unit_test()
BOOST_AUTO_TEST_CASE(ut1) BOOST_AUTO_TEST_CASE(ut1)
{ {
// using namespace mmcif; // using namespace mmcif;
auto f = R"(data_TEST auto f = R"(data_TEST
# #
loop_ loop_
_test.id _test.id
...@@ -91,36 +90,36 @@ _test.name ...@@ -91,36 +90,36 @@ _test.name
3 mies 3 mies
)"_cf; )"_cf;
auto& db = f.firstDatablock(); auto &db = f.firstDatablock();
BOOST_CHECK(db.getName() == "TEST");
auto &test = db["test"];
BOOST_CHECK(test.size() == 3);
BOOST_CHECK(db.getName() == "TEST"); // wrong! the next lines will crash. And that's OK, don't do that
// for (auto r: test)
auto& test = db["test"]; // test.erase(r);
BOOST_CHECK(test.size() == 3);
// wrong! the next lines will crash. And that's OK, don't do that // BOOST_CHECK(test.empty());
// for (auto r: test)
// test.erase(r);
// BOOST_CHECK(test.empty());
// test.purge(); // test.purge();
auto n = test.erase(cif::Key("id") == 1, [](const cif::Row& r) { auto n = test.erase(cif::Key("id") == 1, [](const cif::Row &r)
{
BOOST_CHECK_EQUAL(r["id"].as<int>(), 1); BOOST_CHECK_EQUAL(r["id"].as<int>(), 1);
BOOST_CHECK_EQUAL(r["name"].as<std::string>(), "aap"); BOOST_CHECK_EQUAL(r["name"].as<std::string>(), "aap"); });
});
BOOST_CHECK_EQUAL(n, 1); BOOST_CHECK_EQUAL(n, 1);
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(ut2) BOOST_AUTO_TEST_CASE(ut2)
{ {
// using namespace mmcif; // using namespace mmcif;
auto f = R"(data_TEST auto f = R"(data_TEST
# #
loop_ loop_
_test.id _test.id
...@@ -131,36 +130,36 @@ _test.value ...@@ -131,36 +130,36 @@ _test.value
3 mies 1.2 3 mies 1.2
)"_cf; )"_cf;
auto& db = f.firstDatablock(); auto &db = f.firstDatablock();
BOOST_CHECK(db.getName() == "TEST"); BOOST_CHECK(db.getName() == "TEST");
auto& test = db["test"]; auto &test = db["test"];
BOOST_CHECK(test.size() == 3); BOOST_CHECK(test.size() == 3);
int n = 0; int n = 0;
for (auto r: test.find(cif::Key("name") == "aap")) for (auto r : test.find(cif::Key("name") == "aap"))
{ {
BOOST_CHECK(++n == 1); BOOST_CHECK(++n == 1);
BOOST_CHECK(r["id"].as<int>() == 1); BOOST_CHECK(r["id"].as<int>() == 1);
BOOST_CHECK(r["name"].as<std::string>() == "aap"); BOOST_CHECK(r["name"].as<std::string>() == "aap");
BOOST_CHECK(r["value"].as<float>() == 1.0); BOOST_CHECK(r["value"].as<float>() == 1.0);
} }
auto t = test.find(cif::Key("id") == 1); auto t = test.find(cif::Key("id") == 1);
BOOST_CHECK(not t.empty()); BOOST_CHECK(not t.empty());
BOOST_CHECK(t.front()["name"].as<std::string>() == "aap"); BOOST_CHECK(t.front()["name"].as<std::string>() == "aap");
auto t2 = test.find(cif::Key("value") == 1.2); auto t2 = test.find(cif::Key("value") == 1.2);
BOOST_CHECK(not t2.empty()); BOOST_CHECK(not t2.empty());
BOOST_CHECK(t2.front()["name"].as<std::string>() == "mies"); BOOST_CHECK(t2.front()["name"].as<std::string>() == "mies");
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(d1) BOOST_AUTO_TEST_CASE(d1)
{ {
const char dict[] = R"( const char dict[] = R"(
data_test_dict.dic data_test_dict.dic
_datablock.id test_dict.dic _datablock.id test_dict.dic
_datablock.description _datablock.description
...@@ -253,24 +252,24 @@ save__cat_2.desc ...@@ -253,24 +252,24 @@ save__cat_2.desc
save_ save_
)"; )";
struct membuf : public std::streambuf struct membuf : public std::streambuf
{ {
membuf(char* text, size_t length) membuf(char *text, size_t length)
{ {
this->setg(text, text, text + length); this->setg(text, text, text + length);
} }
} buffer(const_cast<char*>(dict), sizeof(dict) - 1); } buffer(const_cast<char *>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer); std::istream is_dict(&buffer);
cif::Validator validator("test", is_dict); cif::Validator validator("test", is_dict);
cif::File f; cif::File f;
f.setValidator(&validator); f.setValidator(&validator);
// -------------------------------------------------------------------- // --------------------------------------------------------------------
const char data[] = R"( const char data[] = R"(
data_test data_test
loop_ loop_
_cat_1.id _cat_1.id
...@@ -286,48 +285,47 @@ _cat_2.desc ...@@ -286,48 +285,47 @@ _cat_2.desc
1 1 'Een dier' 1 1 'Een dier'
2 1 'Een andere aap' 2 1 'Een andere aap'
3 2 'walnoot bijvoorbeeld' 3 2 'walnoot bijvoorbeeld'
)"; )";
struct data_membuf : public std::streambuf struct data_membuf : public std::streambuf
{ {
data_membuf(char* text, size_t length) data_membuf(char *text, size_t length)
{ {
this->setg(text, text, text + length); this->setg(text, text, text + length);
} }
} data_buffer(const_cast<char*>(data), sizeof(data) - 1); } data_buffer(const_cast<char *>(data), sizeof(data) - 1);
std::istream is_data(&data_buffer); std::istream is_data(&data_buffer);
f.load(is_data); f.load(is_data);
auto& cat1 = f.firstDatablock()["cat_1"]; auto &cat1 = f.firstDatablock()["cat_1"];
auto& cat2 = f.firstDatablock()["cat_2"]; auto &cat2 = f.firstDatablock()["cat_2"];
BOOST_CHECK(cat1.size() == 3); BOOST_CHECK(cat1.size() == 3);
BOOST_CHECK(cat2.size() == 3); BOOST_CHECK(cat2.size() == 3);
cat1.erase(cif::Key("id") == 1); cat1.erase(cif::Key("id") == 1);
BOOST_CHECK(cat1.size() == 2); BOOST_CHECK(cat1.size() == 2);
BOOST_CHECK(cat2.size() == 1); BOOST_CHECK(cat2.size() == 1);
// BOOST_CHECK_THROW(cat2.emplace({ // BOOST_CHECK_THROW(cat2.emplace({
// { "id", 4 }, // { "id", 4 },
// { "parent_id", 4 }, // { "parent_id", 4 },
// { "desc", "moet fout gaan" } // { "desc", "moet fout gaan" }
// }), std::exception); // }), std::exception);
BOOST_CHECK_THROW(cat2.emplace({ BOOST_CHECK_THROW(cat2.emplace({{"id", "vijf"}, // <- invalid value
{ "id", "vijf" }, // <- invalid value {"parent_id", 2},
{ "parent_id", 2 }, {"desc", "moet fout gaan"}}),
{ "desc", "moet fout gaan" } std::exception);
}), std::exception);
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(d2) BOOST_AUTO_TEST_CASE(d2)
{ {
const char dict[] = R"( const char dict[] = R"(
data_test_dict.dic data_test_dict.dic
_datablock.id test_dict.dic _datablock.id test_dict.dic
_datablock.description _datablock.description
...@@ -383,24 +381,24 @@ save__cat_1.c ...@@ -383,24 +381,24 @@ save__cat_1.c
save_ save_
)"; )";
struct membuf : public std::streambuf struct membuf : public std::streambuf
{ {
membuf(char* text, size_t length) membuf(char *text, size_t length)
{ {
this->setg(text, text, text + length); this->setg(text, text, text + length);
} }
} buffer(const_cast<char*>(dict), sizeof(dict) - 1); } buffer(const_cast<char *>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer); std::istream is_dict(&buffer);
cif::Validator validator("test", is_dict); cif::Validator validator("test", is_dict);
cif::File f; cif::File f;
f.setValidator(&validator); f.setValidator(&validator);
// -------------------------------------------------------------------- // --------------------------------------------------------------------
const char data[] = R"( const char data[] = R"(
data_test data_test
loop_ loop_
_cat_1.id _cat_1.id
...@@ -408,39 +406,37 @@ _cat_1.c ...@@ -408,39 +406,37 @@ _cat_1.c
aap Aap aap Aap
noot Noot noot Noot
mies Mies mies Mies
)"; )";
struct data_membuf : public std::streambuf
{
data_membuf(char* text, size_t length)
{
this->setg(text, text, text + length);
}
} data_buffer(const_cast<char*>(data), sizeof(data) - 1);
std::istream is_data(&data_buffer);
f.load(is_data);
auto& cat1 = f.firstDatablock()["cat_1"]; struct data_membuf : public std::streambuf
{
data_membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} data_buffer(const_cast<char *>(data), sizeof(data) - 1);
BOOST_CHECK(cat1.size() == 3); std::istream is_data(&data_buffer);
f.load(is_data);
cat1.erase(cif::Key("id") == "AAP"); auto &cat1 = f.firstDatablock()["cat_1"];
BOOST_CHECK(cat1.size() == 3); BOOST_CHECK(cat1.size() == 3);
cat1.erase(cif::Key("id") == "noot"); cat1.erase(cif::Key("id") == "AAP");
BOOST_CHECK(cat1.size() == 2); BOOST_CHECK(cat1.size() == 3);
cat1.erase(cif::Key("id") == "noot");
BOOST_CHECK(cat1.size() == 2);
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(d3) BOOST_AUTO_TEST_CASE(d3)
{ {
const char dict[] = R"( const char dict[] = R"(
data_test_dict.dic data_test_dict.dic
_datablock.id test_dict.dic _datablock.id test_dict.dic
_datablock.description _datablock.description
...@@ -533,24 +529,24 @@ save__cat_2.desc ...@@ -533,24 +529,24 @@ save__cat_2.desc
save_ save_
)"; )";
struct membuf : public std::streambuf struct membuf : public std::streambuf
{ {
membuf(char* text, size_t length) membuf(char *text, size_t length)
{ {
this->setg(text, text, text + length); this->setg(text, text, text + length);
} }
} buffer(const_cast<char*>(dict), sizeof(dict) - 1); } buffer(const_cast<char *>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer); std::istream is_dict(&buffer);
cif::Validator validator("test", is_dict); cif::Validator validator("test", is_dict);
cif::File f; cif::File f;
f.setValidator(&validator); f.setValidator(&validator);
// -------------------------------------------------------------------- // --------------------------------------------------------------------
const char data[] = R"( const char data[] = R"(
data_test data_test
loop_ loop_
_cat_1.id _cat_1.id
...@@ -569,84 +565,79 @@ _cat_2.desc ...@@ -569,84 +565,79 @@ _cat_2.desc
2 1 . 'Een andere aap' 2 1 . 'Een andere aap'
3 2 noot 'walnoot bijvoorbeeld' 3 2 noot 'walnoot bijvoorbeeld'
4 2 n2 hazelnoot 4 2 n2 hazelnoot
)"; )";
struct data_membuf : public std::streambuf
{
data_membuf(char* text, size_t length)
{
this->setg(text, text, text + length);
}
} data_buffer(const_cast<char*>(data), sizeof(data) - 1);
std::istream is_data(&data_buffer);
f.load(is_data);
auto& cat1 = f.firstDatablock()["cat_1"];
auto& cat2 = f.firstDatablock()["cat_2"];
// check a rename in parent and child
for (auto r: cat1.find(cif::Key("id") == 1)) struct data_membuf : public std::streambuf
{ {
r["id"] = 10; data_membuf(char *text, size_t length)
break; {
} this->setg(text, text, text + length);
}
} data_buffer(const_cast<char *>(data), sizeof(data) - 1);
BOOST_CHECK(cat1.size() == 3); std::istream is_data(&data_buffer);
BOOST_CHECK(cat2.size() == 4); f.load(is_data);
BOOST_CHECK(cat1.find(cif::Key("id") == 1).size() == 0); auto &cat1 = f.firstDatablock()["cat_1"];
BOOST_CHECK(cat1.find(cif::Key("id") == 10).size() == 1); auto &cat2 = f.firstDatablock()["cat_2"];
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 1).size() == 0); // check a rename in parent and child
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 10).size() == 2);
// check a rename in parent and child, this time only one child should be renamed for (auto r : cat1.find(cif::Key("id") == 1))
{
r["id"] = 10;
break;
}
for (auto r: cat1.find(cif::Key("id") == 2)) BOOST_CHECK(cat1.size() == 3);
{ BOOST_CHECK(cat2.size() == 4);
r["id"] = 20;
break;
}
BOOST_CHECK(cat1.size() == 3); BOOST_CHECK(cat1.find(cif::Key("id") == 1).size() == 0);
BOOST_CHECK(cat2.size() == 4); BOOST_CHECK(cat1.find(cif::Key("id") == 10).size() == 1);
BOOST_CHECK(cat1.find(cif::Key("id") == 2).size() == 0); BOOST_CHECK(cat2.find(cif::Key("parent_id") == 1).size() == 0);
BOOST_CHECK(cat1.find(cif::Key("id") == 20).size() == 1); BOOST_CHECK(cat2.find(cif::Key("parent_id") == 10).size() == 2);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 2).size() == 1); // check a rename in parent and child, this time only one child should be renamed
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 20).size() == 1);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 2 and cif::Key("name2") == "noot").size() == 0); for (auto r : cat1.find(cif::Key("id") == 2))
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 2 and cif::Key("name2") == "n2").size() == 1); {
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 20 and cif::Key("name2") == "noot").size() == 1); r["id"] = 20;
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 20 and cif::Key("name2") == "n2").size() == 0); break;
}
BOOST_CHECK(cat1.size() == 3);
BOOST_CHECK(cat2.size() == 4);
BOOST_CHECK(cat1.find(cif::Key("id") == 2).size() == 0);
BOOST_CHECK(cat1.find(cif::Key("id") == 20).size() == 1);
// // -------------------------------------------------------------------- BOOST_CHECK(cat2.find(cif::Key("parent_id") == 2).size() == 1);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 20).size() == 1);
// cat1.erase(cif::Key("id") == 10);
// BOOST_CHECK(cat1.size() == 2); BOOST_CHECK(cat2.find(cif::Key("parent_id") == 2 and cif::Key("name2") == "noot").size() == 0);
// BOOST_CHECK(cat2.size() == 2); BOOST_CHECK(cat2.find(cif::Key("parent_id") == 2 and cif::Key("name2") == "n2").size() == 1);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 20 and cif::Key("name2") == "noot").size() == 1);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 20 and cif::Key("name2") == "n2").size() == 0);
// cat1.erase(cif::Key("id") == 20); // // --------------------------------------------------------------------
// BOOST_CHECK(cat1.size() == 1); // cat1.erase(cif::Key("id") == 10);
// BOOST_CHECK(cat2.size() == 1);
// BOOST_CHECK(cat1.size() == 2);
// BOOST_CHECK(cat2.size() == 2);
// cat1.erase(cif::Key("id") == 20);
// BOOST_CHECK(cat1.size() == 1);
// BOOST_CHECK(cat2.size() == 1);
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(d4) BOOST_AUTO_TEST_CASE(d4)
{ {
const char dict[] = R"( const char dict[] = R"(
data_test_dict.dic data_test_dict.dic
_datablock.id test_dict.dic _datablock.id test_dict.dic
_datablock.description _datablock.description
...@@ -741,24 +732,24 @@ save__cat_2.parent_id3 ...@@ -741,24 +732,24 @@ save__cat_2.parent_id3
)"; )";
struct membuf : public std::streambuf struct membuf : public std::streambuf
{ {
membuf(char* text, size_t length) membuf(char *text, size_t length)
{ {
this->setg(text, text, text + length); this->setg(text, text, text + length);
} }
} buffer(const_cast<char*>(dict), sizeof(dict) - 1); } buffer(const_cast<char *>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer); std::istream is_dict(&buffer);
cif::Validator validator("test", is_dict); cif::Validator validator("test", is_dict);
cif::File f; cif::File f;
f.setValidator(&validator); f.setValidator(&validator);
// -------------------------------------------------------------------- // --------------------------------------------------------------------
const char data[] = R"( const char data[] = R"(
data_test data_test
loop_ loop_
_cat_1.id _cat_1.id
...@@ -787,93 +778,90 @@ _cat_2.parent_id3 ...@@ -787,93 +778,90 @@ _cat_2.parent_id3
11 4 roos roos 11 4 roos roos
12 4 . roos 12 4 . roos
13 4 roos . 13 4 roos .
)"; )";
struct data_membuf : public std::streambuf
{
data_membuf(char* text, size_t length)
{
this->setg(text, text, text + length);
}
} data_buffer(const_cast<char*>(data), sizeof(data) - 1);
std::istream is_data(&data_buffer);
f.load(is_data);
auto& cat1 = f.firstDatablock()["cat_1"];
auto& cat2 = f.firstDatablock()["cat_2"];
// check a rename in parent and child struct data_membuf : public std::streambuf
{
data_membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} data_buffer(const_cast<char *>(data), sizeof(data) - 1);
for (auto r: cat1.find(cif::Key("id") == 1)) std::istream is_data(&data_buffer);
{ f.load(is_data);
r["id"] = 10;
break;
}
BOOST_CHECK(cat1.size() == 4); auto &cat1 = f.firstDatablock()["cat_1"];
BOOST_CHECK(cat2.size() == 13); auto &cat2 = f.firstDatablock()["cat_2"];
BOOST_CHECK(cat1.find(cif::Key("id") == 1).size() == 0); // check a rename in parent and child
BOOST_CHECK(cat1.find(cif::Key("id") == 10).size() == 1);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 1).size() == 1); for (auto r : cat1.find(cif::Key("id") == 1))
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 10).size() == 2); {
r["id"] = 10;
break;
}
BOOST_CHECK(cat1.size() == 4);
BOOST_CHECK(cat2.size() == 13);
for (auto r: cat1.find(cif::Key("id") == 2)) BOOST_CHECK(cat1.find(cif::Key("id") == 1).size() == 0);
{ BOOST_CHECK(cat1.find(cif::Key("id") == 10).size() == 1);
r["id"] = 20;
break;
}
BOOST_CHECK(cat1.size() == 4); BOOST_CHECK(cat2.find(cif::Key("parent_id") == 1).size() == 1);
BOOST_CHECK(cat2.size() == 13); BOOST_CHECK(cat2.find(cif::Key("parent_id") == 10).size() == 2);
BOOST_CHECK(cat1.find(cif::Key("id") == 2).size() == 0); for (auto r : cat1.find(cif::Key("id") == 2))
BOOST_CHECK(cat1.find(cif::Key("id") == 20).size() == 1); {
r["id"] = 20;
break;
}
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 2).size() == 2); BOOST_CHECK(cat1.size() == 4);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 20).size() == 2); BOOST_CHECK(cat2.size() == 13);
BOOST_CHECK(cat1.find(cif::Key("id") == 2).size() == 0);
BOOST_CHECK(cat1.find(cif::Key("id") == 20).size() == 1);
for (auto r: cat1.find(cif::Key("id") == 3)) BOOST_CHECK(cat2.find(cif::Key("parent_id") == 2).size() == 2);
{ BOOST_CHECK(cat2.find(cif::Key("parent_id") == 20).size() == 2);
r["id"] = 30;
break;
}
BOOST_CHECK(cat1.size() == 4); for (auto r : cat1.find(cif::Key("id") == 3))
BOOST_CHECK(cat2.size() == 13); {
r["id"] = 30;
break;
}
BOOST_CHECK(cat1.find(cif::Key("id") == 3).size() == 0); BOOST_CHECK(cat1.size() == 4);
BOOST_CHECK(cat1.find(cif::Key("id") == 30).size() == 1); BOOST_CHECK(cat2.size() == 13);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 3).size() == 2); BOOST_CHECK(cat1.find(cif::Key("id") == 3).size() == 0);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 30).size() == 1); BOOST_CHECK(cat1.find(cif::Key("id") == 30).size() == 1);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 3).size() == 2);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 30).size() == 1);
for (auto r: cat1.find(cif::Key("id") == 4)) for (auto r : cat1.find(cif::Key("id") == 4))
{ {
r["id"] = 40; r["id"] = 40;
break; break;
} }
BOOST_CHECK(cat1.size() == 4); BOOST_CHECK(cat1.size() == 4);
BOOST_CHECK(cat2.size() == 13); BOOST_CHECK(cat2.size() == 13);
BOOST_CHECK(cat1.find(cif::Key("id") == 4).size() == 0); BOOST_CHECK(cat1.find(cif::Key("id") == 4).size() == 0);
BOOST_CHECK(cat1.find(cif::Key("id") == 10).size() == 1); BOOST_CHECK(cat1.find(cif::Key("id") == 10).size() == 1);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 4).size() == 3); BOOST_CHECK(cat2.find(cif::Key("parent_id") == 4).size() == 3);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 40).size() == 0); BOOST_CHECK(cat2.find(cif::Key("parent_id") == 40).size() == 0);
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(d5) BOOST_AUTO_TEST_CASE(d5)
{ {
const char dict[] = R"( const char dict[] = R"(
data_test_dict.dic data_test_dict.dic
_datablock.id test_dict.dic _datablock.id test_dict.dic
_datablock.description _datablock.description
...@@ -965,24 +953,24 @@ cat_2 2 cat_2:cat_1:2 ...@@ -965,24 +953,24 @@ cat_2 2 cat_2:cat_1:2
cat_2 3 cat_2:cat_1:3 cat_2 3 cat_2:cat_1:3
)"; )";
struct membuf : public std::streambuf struct membuf : public std::streambuf
{ {
membuf(char* text, size_t length) membuf(char *text, size_t length)
{ {
this->setg(text, text, text + length); this->setg(text, text, text + length);
} }
} buffer(const_cast<char*>(dict), sizeof(dict) - 1); } buffer(const_cast<char *>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer); std::istream is_dict(&buffer);
cif::Validator validator("test", is_dict); cif::Validator validator("test", is_dict);
cif::File f; cif::File f;
f.setValidator(&validator); f.setValidator(&validator);
// -------------------------------------------------------------------- // --------------------------------------------------------------------
const char data[] = R"( const char data[] = R"(
data_test data_test
loop_ loop_
_cat_1.id _cat_1.id
...@@ -1004,119 +992,120 @@ _cat_2.parent_id3 ...@@ -1004,119 +992,120 @@ _cat_2.parent_id3
7 3 3 3 7 3 3 3
)"; )";
// -------------------------------------------------------------------- // --------------------------------------------------------------------
struct data_membuf : public std::streambuf struct data_membuf : public std::streambuf
{ {
data_membuf(char* text, size_t length) data_membuf(char *text, size_t length)
{ {
this->setg(text, text, text + length); this->setg(text, text, text + length);
} }
} data_buffer(const_cast<char*>(data), sizeof(data) - 1); } data_buffer(const_cast<char *>(data), sizeof(data) - 1);
std::istream is_data(&data_buffer); std::istream is_data(&data_buffer);
f.load(is_data); f.load(is_data);
auto& cat1 = f.firstDatablock()["cat_1"]; auto &cat1 = f.firstDatablock()["cat_1"];
auto& cat2 = f.firstDatablock()["cat_2"]; auto &cat2 = f.firstDatablock()["cat_2"];
// -------------------------------------------------------------------- // --------------------------------------------------------------------
// check iterate children // check iterate children
auto PR2set = cat1.find(cif::Key("id") == 2); auto PR2set = cat1.find(cif::Key("id") == 2);
BOOST_ASSERT(PR2set.size() == 1); BOOST_ASSERT(PR2set.size() == 1);
auto PR2 = PR2set.front(); auto PR2 = PR2set.front();
BOOST_CHECK(PR2["id"].as<int>() == 2); BOOST_CHECK(PR2["id"].as<int>() == 2);
auto CR2set = cat1.getChildren(PR2, "cat_2"); auto CR2set = cat1.getChildren(PR2, "cat_2");
BOOST_ASSERT(CR2set.size() == 3); BOOST_ASSERT(CR2set.size() == 3);
std::vector<int> CRids; std::vector<int> CRids;
std::transform(CR2set.begin(), CR2set.end(), std::back_inserter(CRids), [](cif::Row r) { return r["id"].as<int>(); }); std::transform(CR2set.begin(), CR2set.end(), std::back_inserter(CRids), [](cif::Row r)
std::sort(CRids.begin(), CRids.end()); { return r["id"].as<int>(); });
BOOST_CHECK(CRids == std::vector<int>({ 4, 5, 6})); std::sort(CRids.begin(), CRids.end());
BOOST_CHECK(CRids == std::vector<int>({4, 5, 6}));
// check a rename in parent and child
// check a rename in parent and child
for (auto r: cat1.find(cif::Key("id") == 1))
{ for (auto r : cat1.find(cif::Key("id") == 1))
r["id"] = 10; {
break; r["id"] = 10;
} break;
}
BOOST_CHECK(cat1.size() == 3);
BOOST_CHECK(cat2.size() == 7); BOOST_CHECK(cat1.size() == 3);
BOOST_CHECK(cat2.size() == 7);
BOOST_CHECK(cat1.find(cif::Key("id") == 1).size() == 0);
BOOST_CHECK(cat1.find(cif::Key("id") == 10).size() == 1); BOOST_CHECK(cat1.find(cif::Key("id") == 1).size() == 0);
BOOST_CHECK(cat1.find(cif::Key("id") == 10).size() == 1);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 1).size() == 0);
BOOST_CHECK(cat2.find(cif::Key("parent_id2") == 1).size() == 0); BOOST_CHECK(cat2.find(cif::Key("parent_id") == 1).size() == 0);
BOOST_CHECK(cat2.find(cif::Key("parent_id3") == 1).size() == 0); BOOST_CHECK(cat2.find(cif::Key("parent_id2") == 1).size() == 0);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 10).size() == 1); BOOST_CHECK(cat2.find(cif::Key("parent_id3") == 1).size() == 0);
BOOST_CHECK(cat2.find(cif::Key("parent_id2") == 10).size() == 1); BOOST_CHECK(cat2.find(cif::Key("parent_id") == 10).size() == 1);
BOOST_CHECK(cat2.find(cif::Key("parent_id3") == 10).size() == 1); BOOST_CHECK(cat2.find(cif::Key("parent_id2") == 10).size() == 1);
BOOST_CHECK(cat2.find(cif::Key("parent_id3") == 10).size() == 1);
for (auto r: cat1.find(cif::Key("id") == 2))
{ for (auto r : cat1.find(cif::Key("id") == 2))
r["id"] = 20; {
break; r["id"] = 20;
} break;
}
BOOST_CHECK(cat1.size() == 3);
BOOST_CHECK(cat2.size() == 7); BOOST_CHECK(cat1.size() == 3);
BOOST_CHECK(cat2.size() == 7);
BOOST_CHECK(cat1.find(cif::Key("id") == 2).size() == 0);
BOOST_CHECK(cat1.find(cif::Key("id") == 20).size() == 1); BOOST_CHECK(cat1.find(cif::Key("id") == 2).size() == 0);
BOOST_CHECK(cat1.find(cif::Key("id") == 20).size() == 1);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 2).size() == 0);
BOOST_CHECK(cat2.find(cif::Key("parent_id2") == 2).size() == 0); BOOST_CHECK(cat2.find(cif::Key("parent_id") == 2).size() == 0);
BOOST_CHECK(cat2.find(cif::Key("parent_id3") == 2).size() == 0); BOOST_CHECK(cat2.find(cif::Key("parent_id2") == 2).size() == 0);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 20).size() == 2); BOOST_CHECK(cat2.find(cif::Key("parent_id3") == 2).size() == 0);
BOOST_CHECK(cat2.find(cif::Key("parent_id2") == 20).size() == 2); BOOST_CHECK(cat2.find(cif::Key("parent_id") == 20).size() == 2);
BOOST_CHECK(cat2.find(cif::Key("parent_id3") == 20).size() == 2); BOOST_CHECK(cat2.find(cif::Key("parent_id2") == 20).size() == 2);
BOOST_CHECK(cat2.find(cif::Key("parent_id3") == 20).size() == 2);
for (auto r: cat1.find(cif::Key("id") == 3))
{ for (auto r : cat1.find(cif::Key("id") == 3))
r["id"] = 30; {
break; r["id"] = 30;
} break;
}
BOOST_CHECK(cat1.size() == 3);
BOOST_CHECK(cat2.size() == 7); BOOST_CHECK(cat1.size() == 3);
BOOST_CHECK(cat2.size() == 7);
BOOST_CHECK(cat1.find(cif::Key("id") == 3).size() == 0);
BOOST_CHECK(cat1.find(cif::Key("id") == 30).size() == 1); BOOST_CHECK(cat1.find(cif::Key("id") == 3).size() == 0);
BOOST_CHECK(cat1.find(cif::Key("id") == 30).size() == 1);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 3).size() == 0);
BOOST_CHECK(cat2.find(cif::Key("parent_id2") == 3).size() == 0); BOOST_CHECK(cat2.find(cif::Key("parent_id") == 3).size() == 0);
BOOST_CHECK(cat2.find(cif::Key("parent_id3") == 3).size() == 0); BOOST_CHECK(cat2.find(cif::Key("parent_id2") == 3).size() == 0);
BOOST_CHECK(cat2.find(cif::Key("parent_id") == 30).size() == 1); BOOST_CHECK(cat2.find(cif::Key("parent_id3") == 3).size() == 0);
BOOST_CHECK(cat2.find(cif::Key("parent_id2") == 30).size() == 1); BOOST_CHECK(cat2.find(cif::Key("parent_id") == 30).size() == 1);
BOOST_CHECK(cat2.find(cif::Key("parent_id3") == 30).size() == 1); BOOST_CHECK(cat2.find(cif::Key("parent_id2") == 30).size() == 1);
BOOST_CHECK(cat2.find(cif::Key("parent_id3") == 30).size() == 1);
// test delete
// test delete
cat1.erase(cif::Key("id") == 10);
BOOST_CHECK(cat1.size() == 2); cat1.erase(cif::Key("id") == 10);
BOOST_CHECK(cat2.size() == 4); BOOST_CHECK(cat1.size() == 2);
BOOST_CHECK(cat2.size() == 4);
cat1.erase(cif::Key("id") == 20);
BOOST_CHECK(cat1.size() == 1); cat1.erase(cif::Key("id") == 20);
BOOST_CHECK(cat2.size() == 1); BOOST_CHECK(cat1.size() == 1);
BOOST_CHECK(cat2.size() == 1);
cat1.erase(cif::Key("id") == 30);
BOOST_CHECK(cat1.size() == 0); cat1.erase(cif::Key("id") == 30);
BOOST_CHECK(cat2.size() == 0); BOOST_CHECK(cat1.size() == 0);
BOOST_CHECK(cat2.size() == 0);
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(c1) BOOST_AUTO_TEST_CASE(c1)
{ {
cif::VERBOSE = 1; cif::VERBOSE = 1;
auto f = R"(data_TEST auto f = R"(data_TEST
# #
loop_ loop_
_test.id _test.id
...@@ -1128,52 +1117,52 @@ _test.name ...@@ -1128,52 +1117,52 @@ _test.name
5 ? 5 ?
)"_cf; )"_cf;
auto& db = f.firstDatablock(); auto &db = f.firstDatablock();
for (auto r: db["test"].find(cif::Key("id") == 1)) for (auto r : db["test"].find(cif::Key("id") == 1))
{ {
const auto& [id, name] = r.get<int, std::string>({"id", "name"}); const auto &[id, name] = r.get<int, std::string>({"id", "name"});
BOOST_CHECK(id == 1); BOOST_CHECK(id == 1);
BOOST_CHECK(name == "aap"); BOOST_CHECK(name == "aap");
} }
for (auto r: db["test"].find(cif::Key("id") == 4)) for (auto r : db["test"].find(cif::Key("id") == 4))
{ {
const auto& [id, name] = r.get<int, std::string>({"id", "name"}); const auto &[id, name] = r.get<int, std::string>({"id", "name"});
BOOST_CHECK(id == 4); BOOST_CHECK(id == 4);
BOOST_CHECK(name.empty()); BOOST_CHECK(name.empty());
} }
for (auto r: db["test"].find(cif::Key("id") == 5)) for (auto r : db["test"].find(cif::Key("id") == 5))
{ {
const auto& [id, name] = r.get<int, std::string>({"id", "name"}); const auto &[id, name] = r.get<int, std::string>({"id", "name"});
BOOST_CHECK(id == 5); BOOST_CHECK(id == 5);
BOOST_CHECK(name.empty()); BOOST_CHECK(name.empty());
} }
// optional // optional
for (auto r: db["test"]) for (auto r : db["test"])
{ {
const auto& [id, name] = r.get<int, std::optional<std::string>>({"id", "name"}); const auto &[id, name] = r.get<int, std::optional<std::string>>({"id", "name"});
switch (id) switch (id)
{ {
case 1: BOOST_CHECK(name == "aap"); break; case 1: BOOST_CHECK(name == "aap"); break;
case 2: BOOST_CHECK(name == "noot"); break; case 2: BOOST_CHECK(name == "noot"); break;
case 3: BOOST_CHECK(name == "mies"); break; case 3: BOOST_CHECK(name == "mies"); break;
case 4: case 4:
case 5: BOOST_CHECK(not name); break; case 5: BOOST_CHECK(not name); break;
default: default:
BOOST_CHECK(false); BOOST_CHECK(false);
} }
} }
} }
BOOST_AUTO_TEST_CASE(c2) BOOST_AUTO_TEST_CASE(c2)
{ {
cif::VERBOSE = 1; cif::VERBOSE = 1;
auto f = R"(data_TEST auto f = R"(data_TEST
# #
loop_ loop_
_test.id _test.id
...@@ -1185,31 +1174,30 @@ _test.name ...@@ -1185,31 +1174,30 @@ _test.name
5 ? 5 ?
)"_cf; )"_cf;
auto& db = f.firstDatablock(); auto &db = f.firstDatablock();
// query tests
for (const auto& [id, name]: db["test"].rows<int, std::optional<std::string>>("id", "name"))
{
switch (id)
{
case 1: BOOST_CHECK(name == "aap"); break;
case 2: BOOST_CHECK(name == "noot"); break;
case 3: BOOST_CHECK(name == "mies"); break;
case 4:
case 5: BOOST_CHECK(not name); break;
default:
BOOST_CHECK(false);
}
}
}
// query tests
for (const auto &[id, name] : db["test"].rows<int, std::optional<std::string>>("id", "name"))
{
switch (id)
{
case 1: BOOST_CHECK(name == "aap"); break;
case 2: BOOST_CHECK(name == "noot"); break;
case 3: BOOST_CHECK(name == "mies"); break;
case 4:
case 5: BOOST_CHECK(not name); break;
default:
BOOST_CHECK(false);
}
}
}
BOOST_AUTO_TEST_CASE(c3) BOOST_AUTO_TEST_CASE(c3)
{ {
cif::VERBOSE = 1; cif::VERBOSE = 1;
auto f = R"(data_TEST auto f = R"(data_TEST
# #
loop_ loop_
_test.id _test.id
...@@ -1221,27 +1209,27 @@ _test.name ...@@ -1221,27 +1209,27 @@ _test.name
5 ? 5 ?
)"_cf; )"_cf;
auto& db = f.firstDatablock(); auto &db = f.firstDatablock();
// query tests // query tests
for (const auto& [id, name]: db["test"].find<int, std::optional<std::string>>(cif::All(), "id", "name")) for (const auto &[id, name] : db["test"].find<int, std::optional<std::string>>(cif::All(), "id", "name"))
{ {
switch (id) switch (id)
{ {
case 1: BOOST_CHECK(name == "aap"); break; case 1: BOOST_CHECK(name == "aap"); break;
case 2: BOOST_CHECK(name == "noot"); break; case 2: BOOST_CHECK(name == "noot"); break;
case 3: BOOST_CHECK(name == "mies"); break; case 3: BOOST_CHECK(name == "mies"); break;
case 4: case 4:
case 5: BOOST_CHECK(not name); break; case 5: BOOST_CHECK(not name); break;
default: default:
BOOST_CHECK(false); BOOST_CHECK(false);
} }
} }
const auto& [id, name] = db["test"].find1<int, std::string>(cif::Key("id") == 1, "id", "name"); const auto &[id, name] = db["test"].find1<int, std::string>(cif::Key("id") == 1, "id", "name");
BOOST_CHECK(id == 1); BOOST_CHECK(id == 1);
BOOST_CHECK(name == "aap"); BOOST_CHECK(name == "aap");
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -1250,22 +1238,22 @@ _test.name ...@@ -1250,22 +1238,22 @@ _test.name
BOOST_AUTO_TEST_CASE(r1) BOOST_AUTO_TEST_CASE(r1)
{ {
/* /*
Rationale: Rationale:
The pdbx_mmcif dictionary contains inconsistent child-parent relations. E.g. atom_site is parent The pdbx_mmcif dictionary contains inconsistent child-parent relations. E.g. atom_site is parent
of pdbx_nonpoly_scheme which itself is a parent of pdbx_entity_nonpoly. If I want to rename a residue of pdbx_nonpoly_scheme which itself is a parent of pdbx_entity_nonpoly. If I want to rename a residue
I cannot update pdbx_nonpoly_scheme since changing a parent changes children, but not vice versa. I cannot update pdbx_nonpoly_scheme since changing a parent changes children, but not vice versa.
But if I change the comp_id in atom_site, the pdbx_nonpoly_scheme is update, that's good, and then But if I change the comp_id in atom_site, the pdbx_nonpoly_scheme is update, that's good, and then
pdbx_entity_nonpoly is updated and that's bad. pdbx_entity_nonpoly is updated and that's bad.
The idea is now that if we update a parent and a child that must change as well, we first check The idea is now that if we update a parent and a child that must change as well, we first check
if there are more parents of this child that will not change. In that case we have to split the if there are more parents of this child that will not change. In that case we have to split the
child into two, one with the new value and one with the old. We then of course have to split all child into two, one with the new value and one with the old. We then of course have to split all
children of this split row that are direct children. children of this split row that are direct children.
*/ */
const char dict[] = R"( const char dict[] = R"(
data_test_dict.dic data_test_dict.dic
_datablock.id test_dict.dic _datablock.id test_dict.dic
_datablock.description _datablock.description
...@@ -1394,23 +1382,23 @@ cat_2 1 '_cat_2.num' '_cat_3.num' cat_3 ...@@ -1394,23 +1382,23 @@ cat_2 1 '_cat_2.num' '_cat_3.num' cat_3
)"; )";
struct membuf : public std::streambuf struct membuf : public std::streambuf
{ {
membuf(char* text, size_t length) membuf(char *text, size_t length)
{ {
this->setg(text, text, text + length); this->setg(text, text, text + length);
} }
} buffer(const_cast<char*>(dict), sizeof(dict) - 1); } buffer(const_cast<char *>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer); std::istream is_dict(&buffer);
cif::Validator validator("test", is_dict); cif::Validator validator("test", is_dict);
cif::File f; cif::File f;
f.setValidator(&validator); f.setValidator(&validator);
// -------------------------------------------------------------------- // --------------------------------------------------------------------
const char data[] = R"( const char data[] = R"(
data_test data_test
loop_ loop_
_cat_1.id _cat_1.id
...@@ -1435,29 +1423,29 @@ _cat_3.name ...@@ -1435,29 +1423,29 @@ _cat_3.name
_cat_3.num _cat_3.num
1 aap 1 1 aap 1
2 aap 2 2 aap 2
)"; )";
using namespace cif::literals; using namespace cif::literals;
struct data_membuf : public std::streambuf struct data_membuf : public std::streambuf
{ {
data_membuf(char* text, size_t length) data_membuf(char *text, size_t length)
{ {
this->setg(text, text, text + length); this->setg(text, text, text + length);
} }
} data_buffer(const_cast<char*>(data), sizeof(data) - 1); } data_buffer(const_cast<char *>(data), sizeof(data) - 1);
std::istream is_data(&data_buffer); std::istream is_data(&data_buffer);
f.load(is_data); f.load(is_data);
auto& cat1 = f.firstDatablock()["cat_1"]; auto &cat1 = f.firstDatablock()["cat_1"];
auto& cat2 = f.firstDatablock()["cat_2"]; auto &cat2 = f.firstDatablock()["cat_2"];
auto& cat3 = f.firstDatablock()["cat_3"]; auto &cat3 = f.firstDatablock()["cat_3"];
cat3.update_value("name"_key == "aap" and "num"_key == 1, "name", "aapje"); cat3.update_value("name"_key == "aap" and "num"_key == 1, "name", "aapje");
BOOST_CHECK(cat3.size() == 2); BOOST_CHECK(cat3.size() == 2);
{ {
int id, num; int id, num;
std::string name; std::string name;
...@@ -1471,9 +1459,9 @@ _cat_3.num ...@@ -1471,9 +1459,9 @@ _cat_3.num
BOOST_CHECK(num == 2); BOOST_CHECK(num == 2);
BOOST_CHECK(name == "aap"); BOOST_CHECK(name == "aap");
} }
int i = 0; int i = 0;
for (const auto &[id, name, num, desc]: cat2.rows<int,std::string,int,std::string>("id", "name", "num", "desc")) for (const auto &[id, name, num, desc] : cat2.rows<int, std::string, int, std::string>("id", "name", "num", "desc"))
{ {
switch (++i) switch (++i)
{ {
...@@ -1497,7 +1485,7 @@ _cat_3.num ...@@ -1497,7 +1485,7 @@ _cat_3.num
BOOST_CHECK(name == "noot"); BOOST_CHECK(name == "noot");
BOOST_CHECK(desc == "walnoot bijvoorbeeld"); BOOST_CHECK(desc == "walnoot bijvoorbeeld");
break; break;
default: default:
BOOST_FAIL("Unexpected record"); BOOST_FAIL("Unexpected record");
} }
...@@ -1505,7 +1493,7 @@ _cat_3.num ...@@ -1505,7 +1493,7 @@ _cat_3.num
BOOST_CHECK(cat1.size() == 4); BOOST_CHECK(cat1.size() == 4);
i = 0; i = 0;
for (const auto &[id, name, desc]: cat1.rows<int,std::string,std::string>("id", "name", "desc")) for (const auto &[id, name, desc] : cat1.rows<int, std::string, std::string>("id", "name", "desc"))
{ {
switch (++i) switch (++i)
{ {
...@@ -1526,13 +1514,13 @@ _cat_3.num ...@@ -1526,13 +1514,13 @@ _cat_3.num
BOOST_CHECK(name == "mies"); BOOST_CHECK(name == "mies");
BOOST_CHECK(desc == "Mies"); BOOST_CHECK(desc == "Mies");
break; break;
case 4: case 4:
BOOST_CHECK(id == 4); BOOST_CHECK(id == 4);
BOOST_CHECK(name == "aap"); BOOST_CHECK(name == "aap");
BOOST_CHECK(desc == "Aap"); BOOST_CHECK(desc == "Aap");
break; break;
default: default:
BOOST_FAIL("Unexpected record"); BOOST_FAIL("Unexpected record");
} }
...@@ -1545,7 +1533,7 @@ _cat_3.num ...@@ -1545,7 +1533,7 @@ _cat_3.num
BOOST_AUTO_TEST_CASE(bondmap_1) BOOST_AUTO_TEST_CASE(bondmap_1)
{ {
cif::VERBOSE = 2; cif::VERBOSE = 2;
// sections taken from CCD compounds.cif // sections taken from CCD compounds.cif
auto components = R"( auto components = R"(
...@@ -1634,7 +1622,7 @@ PRO CD HD3 SING N N 16 ...@@ -1634,7 +1622,7 @@ PRO CD HD3 SING N N 16
PRO OXT HXT SING N N 17 PRO OXT HXT SING N N 17
)"_cf; )"_cf;
const std::filesystem::path example(gTestDir / ".."/"examples"/"1cbs.cif.gz"); const std::filesystem::path example(gTestDir / ".." / "examples" / "1cbs.cif.gz");
mmcif::File file(example.string()); mmcif::File file(example.string());
mmcif::Structure structure(file); mmcif::Structure structure(file);
...@@ -1642,11 +1630,11 @@ PRO OXT HXT SING N N 17 ...@@ -1642,11 +1630,11 @@ PRO OXT HXT SING N N 17
mmcif::BondMap bm(structure); mmcif::BondMap bm(structure);
// Test the bonds of the first three residues, that's PRO A 1, ASN A 2, PHE A 3 // Test the bonds of the first three residues, that's PRO A 1, ASN A 2, PHE A 3
for (const auto& [compound, seqnr]: std::initializer_list<std::tuple<std::string,int>>{ { "PRO", 1 }, { "ASN", 2 }, { "PHE", 3 } }) for (const auto &[compound, seqnr] : std::initializer_list<std::tuple<std::string, int>>{{"PRO", 1}, {"ASN", 2}, {"PHE", 3}})
{ {
auto& res = structure.getResidue("A", compound, seqnr); auto &res = structure.getResidue("A", compound, seqnr);
auto atoms = res.atoms(); auto atoms = res.atoms();
auto dc = components.get(compound); auto dc = components.get(compound);
...@@ -1655,14 +1643,14 @@ PRO OXT HXT SING N N 17 ...@@ -1655,14 +1643,14 @@ PRO OXT HXT SING N N 17
auto cc = dc->get("chem_comp_bond"); auto cc = dc->get("chem_comp_bond");
BOOST_ASSERT(cc != nullptr); BOOST_ASSERT(cc != nullptr);
std::set<std::tuple<std::string,std::string>> bonded; std::set<std::tuple<std::string, std::string>> bonded;
for (const auto& [atom_id_1, atom_id_2]: cc->rows<std::string,std::string>("atom_id_1", "atom_id_2")) for (const auto &[atom_id_1, atom_id_2] : cc->rows<std::string, std::string>("atom_id_1", "atom_id_2"))
{ {
if (atom_id_1 > atom_id_2) if (atom_id_1 > atom_id_2)
bonded.insert({ atom_id_2, atom_id_1 }); bonded.insert({atom_id_2, atom_id_1});
else else
bonded.insert({ atom_id_1, atom_id_2 }); bonded.insert({atom_id_1, atom_id_2});
} }
for (size_t i = 0; i + 1 < atoms.size(); ++i) for (size_t i = 0; i + 1 < atoms.size(); ++i)
...@@ -1677,8 +1665,8 @@ PRO OXT HXT SING N N 17 ...@@ -1677,8 +1665,8 @@ PRO OXT HXT SING N N 17
bool bonded_1_i = bm(atoms[j], atoms[i]); bool bonded_1_i = bm(atoms[j], atoms[i]);
bool bonded_t = label_i > label_j bool bonded_t = label_i > label_j
? bonded.count({ label_j, label_i }) ? bonded.count({label_j, label_i})
: bonded.count({ label_i, label_j }); : bonded.count({label_i, label_j});
BOOST_CHECK(bonded_1 == bonded_t); BOOST_CHECK(bonded_1 == bonded_t);
BOOST_CHECK(bonded_1_i == bonded_t); BOOST_CHECK(bonded_1_i == bonded_t);
...@@ -1718,20 +1706,19 @@ BOOST_AUTO_TEST_CASE(t1) ...@@ -1718,20 +1706,19 @@ BOOST_AUTO_TEST_CASE(t1)
// q = Normalize(q); // q = Normalize(q);
// Quaternion q{ 0.1, 0.2, 0.3, 0.4 }; // Quaternion q{ 0.1, 0.2, 0.3, 0.4 };
Quaternion q{ 0.5, 0.5, 0.5, 0.5 }; Quaternion q{0.5, 0.5, 0.5, 0.5};
q = Normalize(q); q = Normalize(q);
const auto &&[angle0, axis0] = QuaternionToAngleAxis(q); const auto &&[angle0, axis0] = QuaternionToAngleAxis(q);
std::vector<Point> p1{ std::vector<Point> p1{
{ 16.979, 13.301, 44.555 }, {16.979, 13.301, 44.555},
{ 18.150, 13.525, 43.680 }, {18.150, 13.525, 43.680},
{ 18.656, 14.966, 43.784 }, {18.656, 14.966, 43.784},
{ 17.890, 15.889, 44.078 }, {17.890, 15.889, 44.078},
{ 17.678, 13.270, 42.255 }, {17.678, 13.270, 42.255},
{ 16.248, 13.734, 42.347 }, {16.248, 13.734, 42.347},
{ 15.762, 13.216, 43.724 } {15.762, 13.216, 43.724}};
};
auto p2 = p1; auto p2 = p1;
...@@ -1739,7 +1726,7 @@ BOOST_AUTO_TEST_CASE(t1) ...@@ -1739,7 +1726,7 @@ BOOST_AUTO_TEST_CASE(t1)
for (auto &p : p2) for (auto &p : p2)
p.rotate(q); p.rotate(q);
CenterPoints(p2); CenterPoints(p2);
auto q2 = AlignPoints(p1, p2); auto q2 = AlignPoints(p1, p2);
...@@ -1757,3 +1744,38 @@ BOOST_AUTO_TEST_CASE(t1) ...@@ -1757,3 +1744,38 @@ BOOST_AUTO_TEST_CASE(t1)
// std::cout << "rmsd: " << RMSd(p1, p2) << std::endl; // std::cout << "rmsd: " << RMSd(p1, p2) << std::endl;
} }
BOOST_AUTO_TEST_CASE(parser_test_1)
{
auto data1 = R"(
data_QM
_test.text ??
)"_cf;
auto &db1 = data1.firstDatablock();
auto &test1 = db1["test"];
BOOST_CHECK_EQUAL(test1.size(), 1);
for (auto r : test1)
{
const auto &[text] = r.get<std::string>({"text"});
BOOST_CHECK_EQUAL(text, "??");
}
std::stringstream ss;
data1.save(ss);
auto data2 = cif::File(ss);
auto &db2 = data2.firstDatablock();
auto &test2 = db2["test"];
BOOST_CHECK_EQUAL(test2.size(), 1);
for (auto r : test2)
{
const auto &[text] = r.get<std::string>({"text"});
BOOST_CHECK_EQUAL(text, "??");
}
}
\ No newline at end of file
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